Funny, I could sing that same "story in this game sucks"-hymn about pretty much every other AAA title. Assassin's Creed at least attempted to spin a rich background story. The catch? It is all still tied to people using the Animus and present day shenanigans.
However, Desmond's story is apparently OVER, so no more dickface to worry about.
I never gave a shit about Desmond's part of the story after the initial game, which ended on a "HOLY FUCK, 16 KNEW IT ALL ALONG!!!"-note. Then they killed 16, and then they killed 16's Animus left-overs because Desmond needed some guidance while being dumb and in a coma.
Part of the problem was that Desmond was an unlikeable twat. Another part of it was that the story was pretty much about a small group of Assassins on the run to save the world while trying to escape the Templars. Shit grew old very quickly since it took them AC2, Brotherhood, Revelations AND AC3 to achieve that; baby steps, year after year.
Yet another reason was that none of the present-day locations where even remotely as interesting as their counterparts in the past.
They obviously wanted a Scifi story. They needed it at some point, but then it just became the framework in which to piece the database entries and events into, while the present day timeline got more and more tedious and rooted to the spot.
The past timelines and sequences were suffering from some disjointed events, often due to the player being pulled back into the present day due to some bogus.
However, scope and feel of the past timelines, especially the Ezio ones, were amazingly well done. Yes, there was a lot to nitpick about here and there, but the overall performance was absolutely great. There's a good reason almost every AC game won awards for the story department.
AC3 rant incoming!
Now, AC3 was a different beast entirely. It was shallow, self-centered, lacked vision and was even more repetitive than AC1, which was tedious in most aspects and is more to be seen as an elaborate tech-demo of what is possible on the new generation of hardware.
But AC3 was neither polished nor thought through well enough to excite much. The characters were flat, the protagonist an ignorant bastard who wouldn't stop to think for a moment and the overarcing gameplay elements, like the assassin recruits, were neglected and not strongly enough incorporated into the storyline.
Connor never really achieved anything. He was a bystander throughout the whole game, watching other people making decisions, staying his blade when faced with his nemesis due to other people being around, being guided the whole game, driven by nothing but childish whims.
You know who wanted vengeance for his family's death? Ezio Auditore da Firenze. You know who outgrew it after enough consideration and later dedicated his life to fighting against oppression and a bigger cause than his personal reasons? Ezio Auditore da Firenze.
You know who didn't manage that? Connor.
Neither of those two got professional training as an assassin before they were in their late teens, and Ezio got little to no guidance in the first place, while Connor's training was never actually shown in AC3. Meanwhile Ezio grew with the storyline of AC2 and continued to learn more in Brotherhood, and even after he became Mentor to the Order.
Connor rejected advice, acted like a spoiled brat and let the important things fall below the table in his quest to become a real man.
No wonder nobody liked AC3 and is looking forward to the Ezio-team getting back with AC4.